Sodium in PDB 4iib: Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus

All present enzymatic activity of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus:
3.2.1.21;

The structure of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus, PDB code: 4iib was solved by K.Suzuki, J.Sumitani, T.Kawaguchi, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.49 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.162, 123.024, 222.254, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 16.9

The binding sites of Sodium atom in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus (pdb code 4iib). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus, PDB code: 4iib:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na944 b:17.0 occ:1.00 OD1 A:ASN539 2.3 22.9 1.0 O A:HOH1980 2.3 22.4 1.0 O A:HOH1979 2.4 28.7 1.0 O3 A:NAG933 2.4 15.4 1.0 O A:ASN539 2.5 10.3 1.0 O7 A:NAG933 2.6 16.7 1.0 CG A:ASN539 3.2 21.5 1.0 C7 A:NAG933 3.4 13.3 1.0 C A:ASN539 3.5 11.9 1.0 C3 A:NAG933 3.5 13.2 1.0 C2 A:NAG933 3.5 11.9 1.0 CA A:ASN539 3.7 11.5 1.0 N2 A:NAG933 3.9 13.4 1.0 ND2 A:ASN539 3.9 26.3 1.0 O5 A:NAG934 4.0 18.0 1.0 CB A:ASN539 4.1 15.8 1.0 C4 A:NAG933 4.1 12.3 1.0 O A:HOH1978 4.1 30.5 1.0 C5 A:NAG934 4.3 20.1 1.0 C6 A:NAG934 4.4 21.9 1.0 C1 A:NAG934 4.6 18.7 1.0 C8 A:NAG933 4.6 18.8 1.0 O A:HOH1620 4.7 48.2 1.0 N A:ASN540 4.7 9.9 1.0 O4 A:NAG933 4.8 14.4 1.0 O A:HOH1982 4.9 41.3 1.0 O A:HOH1362 4.9 22.9 1.0 C1 A:NAG933 5.0 12.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Beta-Glucosidase 1 From Aspergillus Aculeatus within 5.0Å range: probe atom residue distance (Å) B Occ B:Na950 b:20.5 occ:1.00 O B:HOH1927 2.3 24.5 1.0 OD1 B:ASN539 2.3 26.1 1.0 O3 B:NAG938 2.4 15.4 1.0 O7 B:NAG938 2.4 18.7 1.0 O B:ASN539 2.5 11.8 1.0 O B:HOH2073 2.5 26.5 1.0 CG B:ASN539 3.2 23.9 1.0 C7 B:NAG938 3.4 14.6 1.0 C B:ASN539 3.4 13.7 1.0 C3 B:NAG938 3.5 12.3 1.0 C2 B:NAG938 3.5 11.9 1.0 CA B:ASN539 3.7 14.7 1.0 N2 B:NAG938 3.8 13.9 1.0 ND2 B:ASN539 4.0 25.4 1.0 CB B:ASN539 4.0 17.9 1.0 C4 B:NAG938 4.0 13.2 1.0 O5 B:NAG939 4.1 22.0 1.0 O B:HOH2044 4.2 26.9 1.0 C5 B:NAG939 4.5 22.4 1.0 C8 B:NAG938 4.6 18.0 1.0 C1 B:NAG939 4.6 19.1 1.0 C6 B:NAG939 4.6 23.5 1.0 O B:HOH1751 4.6 42.1 1.0 N B:ASN540 4.7 11.2 1.0 O B:HOH1542 4.8 15.7 1.0 O4 B:NAG938 4.8 15.2 1.0 C1 B:NAG938 4.9 12.1 1.0

K.Suzuki, J.Sumitani, Y.W.Nam, T.Nishimaki, S.Tani, T.Wakagi, T.Kawaguchi, S.Fushinobu. Crystal Structures of Glycoside Hydrolase Family 3 Beta-Glucosidase 1 From Aspergillus Aculeatus Biochem.J. V. 452 211 2013.
ISSN: ISSN 0264-6021
PubMed: 23537284
DOI: 10.1042/BJ20130054